Question: Job submission failed
0
gravatar for scwoll
3.5 years ago by
scwoll0
United States
scwoll0 wrote:

I am trying to run cufflinks on a dataset, but the job submission fails every time I attempt to do so no matter the perimeters. I have run cufflinks on this data prior to now, but when back and did some different trimming, but other than that it is the same dataset. I don't know if the updates today have anything to do with the issue. 

The error message reads:

{
    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.6",
    "tool_version": "0.0.6",
    "inputs": {
        "input": {
            "batch": false,
            "values": [
                {
                    "id": "bbd44e69cb8906b592a299d43a1faf58",
                    "src": "hda"
                }
            ]
        },
        "max_intron_len": "300000",
        "min_isoform_fraction": "0.1",
        "pre_mrna_fraction": "0.15",
        "do_normalization": "No",
        "reference_annotation|use_ref": "Use reference annotation",
        "reference_annotation|reference_annotation_file": {
            "batch": false,
            "values": [
                {
                    "id": "bbd44e69cb8906b5e6246418c3b32a6b",
                    "src": "hda"
                }
            ]
        },
        "bias_correction|do_bias_correction": "No",
        "multiread_correct": "No",
        "effective_length_correction": "",
        "global_model": ""
    }
}

rna-seq cufflinks • 1.1k views
ADD COMMENTlink modified 3.5 years ago by Jennifer Hillman Jackson25k • written 3.5 years ago by scwoll0
1
gravatar for Jennifer Hillman Jackson
3.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This was occuring on the public Main Galaxy instance at http://usegalaxy.org? If so, the issue has been resolved. Please try the tool again now (more changes were just made recently).

If it fails again, please submit this as a bug report and we can take a closer look. Include a link to this biostar post in the comments. Please leave the error and all inputs undeleted. 

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.5 years ago by Jennifer Hillman Jackson25k
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